Contacts of the helix formed by residues 173 - 189 (chain B) in PDB entry 4HYJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B TYR* 5.3 2.2 - - - +
171B ASN 4.6 2.0 - - - +
172B LYS* 1.3 100.3 - - + +
174B ALA* 1.3 68.0 + - - +
175B PRO* 3.3 4.3 - - + -
176B ILE* 3.0 25.8 + - + -
177B ARG 3.0 5.4 + - - -
239B MET* 3.7 31.0 - - + -
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LYS 3.7 1.4 + - - -
173B PRO* 1.3 69.8 - - - +
175B PRO* 1.3 66.1 - - + +
177B ARG* 3.2 12.9 + - - +
178B ASP* 2.8 44.5 + - - +
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Residues in contact with PRO 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PRO* 3.4 6.5 - - + +
174B ALA* 1.3 94.7 - - + +
176B ILE* 1.3 60.0 + - - +
178B ASP* 3.6 7.2 + - + +
179B ALA* 3.1 16.8 + - - +
235B ALA* 3.4 21.9 - - + +
238B THR* 4.0 25.8 - - + -
239B MET* 3.7 26.5 - - + -
242B LEU* 4.8 6.7 - - + -
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 4.1 11.4 - - + +
100B LEU* 3.7 47.3 - - + +
172B LYS* 3.8 21.1 - - + -
173B PRO* 3.0 19.8 + - + +
175B PRO* 1.3 73.6 - - - +
177B ARG* 1.3 66.8 + - - +
179B ALA* 3.3 2.6 + - - +
180B LEU* 3.0 32.9 + - + +
235B ALA* 4.3 9.4 - - + -
236B VAL* 4.1 12.6 - - + -
239B MET* 3.8 28.5 - - + -
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ALA* 3.4 28.9 - - + +
170B GLU* 2.5 44.7 + - - +
172B LYS* 4.0 7.8 - - - +
173B PRO 3.0 10.9 + - - +
174B ALA* 3.4 13.0 - - - +
176B ILE* 1.3 78.7 - - - +
178B ASP* 1.3 79.7 + - - +
180B LEU* 3.4 8.7 + - - +
181B LEU* 3.1 48.5 + - + +
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Residues in contact with ASP 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ALA* 2.8 34.8 + - - +
175B PRO* 4.0 6.7 - - + +
176B ILE 3.3 0.2 - - - -
177B ARG* 1.3 92.8 + - - +
179B ALA* 1.3 64.4 + - - +
181B LEU* 3.3 8.1 + - - +
182B LYS* 3.0 33.4 + - + +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.9 1.3 - - + -
175B PRO 3.1 19.1 + - - +
176B ILE* 3.3 3.3 + - - +
178B ASP* 1.3 77.0 - - - +
180B LEU* 1.3 53.0 + - - +
182B LYS* 3.2 5.2 + - - +
183B MET* 2.7 53.8 + - + +
231B ILE* 4.1 21.8 - - + +
232B ALA* 4.8 0.4 - - - -
235B ALA* 3.6 20.6 - - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.8 46.3 - - + +
100B LEU* 3.9 14.4 - - + -
101B LEU* 3.6 26.7 - - + -
165B VAL* 4.2 11.6 - - + +
169B ALA* 3.9 21.5 - - + -
172B LYS* 4.3 1.3 - - + -
176B ILE* 3.0 36.7 + - + +
177B ARG 3.6 4.3 - - - +
179B ALA* 1.3 77.0 - - - +
181B LEU* 1.3 64.4 + - + +
183B MET* 3.2 13.6 + - + +
184B ARG* 3.2 26.3 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B VAL* 6.5 0.2 - - + -
166B THR* 4.1 23.1 - - + +
169B ALA* 4.5 7.9 - - + -
170B GLU* 4.6 2.2 - - - +
177B ARG* 3.1 57.8 + - + +
178B ASP* 3.8 6.3 - - - +
179B ALA 3.3 0.4 - - - -
180B LEU* 1.3 76.9 - - - +
182B LYS* 1.3 61.6 + - + +
183B MET 3.6 0.2 + - - -
184B ARG* 2.8 62.0 + - - +
185B LEU* 4.2 5.9 + - - +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASP* 3.0 26.2 + - + +
179B ALA* 3.6 4.5 - - - +
181B LEU* 1.3 75.2 - - + +
183B MET* 1.3 64.2 + - - +
185B LEU* 3.0 33.0 + - + +
186B PHE* 3.8 10.6 - - + -
231B ILE* 4.5 22.2 - - + -
311B LFA 4.8 10.6 - - + +
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Residues in contact with MET 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS* 5.1 5.2 - - - +
97B PHE* 3.6 20.5 - - + -
100B LEU* 3.1 30.1 - - + -
179B ALA* 2.7 49.8 + - + +
180B LEU* 3.2 17.2 + - + +
182B LYS* 1.3 73.5 - - - +
184B ARG* 1.3 63.4 + - - +
186B PHE* 3.1 26.7 + - + +
187B ILE 3.7 2.3 + - - -
228B PHE* 3.6 33.0 - - + +
231B ILE* 4.0 15.5 - - + -
232B ALA* 3.8 24.5 - - + -
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.8 14.7 - - + -
161B LEU* 3.6 24.0 - - + +
162B PHE* 3.6 43.8 - - + -
165B VAL* 5.2 3.1 - - + -
166B THR* 2.7 44.8 + - - +
180B LEU 3.2 14.6 - - - +
181B LEU* 2.8 47.5 + - - +
182B LYS 3.2 0.2 - - - -
183B MET* 1.3 78.2 - - - +
185B LEU* 1.3 58.5 + - - +
187B ILE* 3.1 5.0 + - - +
188B LEU* 2.9 28.6 + - - +
307B LFA 5.7 0.8 - - - +
310B LFA 4.2 20.2 - - - +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B PHE* 4.5 10.1 - - + -
181B LEU 4.3 7.6 - - - +
182B LYS* 3.0 23.4 + - + +
184B ARG* 1.3 75.5 - - - +
186B PHE* 1.3 57.0 + - - +
188B LEU* 4.3 5.6 - - + -
189B ILE* 2.6 53.9 + - + +
310B LFA 3.6 40.6 - - + -
311B LFA 4.0 33.0 - - + -
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Residues in contact with PHE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B LYS* 3.8 12.8 - - + -
183B MET* 3.1 15.8 + - - +
185B LEU* 1.3 79.3 - - - +
187B ILE* 1.3 54.8 + - + +
190B GLY* 2.8 10.7 + - - +
191B TRP* 2.7 36.1 + - + +
223B THR* 3.4 34.8 - - + -
224B ASN* 3.8 18.8 - - - +
227B GLY* 4.1 3.1 - - - -
228B PHE* 3.5 42.0 - + + -
231B ILE* 3.9 27.8 - - + -
311B LFA 3.8 32.3 - - + +
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 5.7 0.2 - - + -
94B LEU* 3.6 21.1 - - + -
97B PHE* 4.2 8.3 - - + -
154B TRP* 3.0 26.1 + - + +
157B ILE* 4.1 11.9 - - + -
158B ILE* 3.9 15.9 - - + +
161B LEU* 3.6 27.4 - - + -
183B MET 3.7 3.6 + - - +
184B ARG 3.1 4.6 + - - +
186B PHE* 1.3 77.5 - - + +
188B LEU* 1.3 61.8 + - - +
191B TRP* 3.3 43.1 - - + +
228B PHE* 3.9 28.7 - - + -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TRP* 3.6 6.4 - - + -
158B ILE* 3.8 30.0 - - + +
162B PHE* 3.8 28.3 - - + -
184B ARG 2.9 15.2 + - - +
185B LEU* 3.8 5.8 - - + +
187B ILE* 1.3 81.2 - - - +
189B ILE* 1.3 67.2 + - + +
192B ALA* 3.6 17.5 - - - +
307B LFA 4.0 27.1 - - + -
308B LFA 4.2 14.4 - - + -
310B LFA 4.3 20.9 - - + -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B LEU* 2.6 40.5 + - + +
188B LEU* 1.3 86.9 - - + +
190B GLY* 1.3 66.8 + - - +
191B TRP 3.2 1.1 - - - -
192B ALA* 3.2 18.0 + - + +
193B ILE* 4.0 8.0 + - - +
310B LFA 4.8 16.4 - - + -
311B LFA 4.1 25.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il